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Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
Several implicit (continuum) solvent models are considered: the Polarized Continuum Model (PCM), the Surface Generalized Born model (SGB), and the COnductor-like Screening model (COSMO) as well as their implementation in the form of the…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
To include the bound electron effects in particle-in-cell (PIC) simulation, we propose a model in which the response of the dipole components of partially ionized ions to external electromagnetic fields can be included. Instead of treating…
We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with…
A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equations that arise in mathematical models for the electrostatics of molecules in solvent. The proposed method used an implicit…
Computed Tomography (CT) is widely used in healthcare for detailed imaging. However, Low-dose CT, despite reducing radiation exposure, often results in images with compromised quality due to increased noise. Traditional methods, including…
The static friction between crystalline surfaces separated by a molecularly thin layer of adsorbed molecules is calculated using molecular dynamics simulations. These molecules naturally lead to a finite static friction that is consistent…
Chemical potential of species in solution is essential for understanding various chemical processes at interfaces. Molecular dynamics (MD) simulations, constrained by fixed compositions, cannot satisfy a constant chemical potential…
The immersed boundary method is a mathematical formulation and numerical method for solving fluid-structure interaction problems. For many biological problems, such as models that include the cell membrane, the immersed structure is a…
Understanding the flow of deformable particles such as liquid drops, synthetic capsules and vesicles, and biological cells confined in a small channel is essential to a wide range of potential chemical and biomedical engineering…
I give an overview of rare event simulation techniques to generate dynamical pathways across high free energy barriers. The methods on which I will concentrate are the reactive flux approach, transition path sampling, (replica-exchange)…
We study the effective forces acting between colloidal particles trapped at a fluid interface which itself is exposed to a pressure field. To this end we apply what we call the ``force approach'', which relies solely on the condition of…
We present a general procedure to introduce electronic polarization into classical Molecular Dynamics (MD) force-fields using a Neural Network (NN) model. We apply this framework to the simulation of a solid-liquid interface where the…
Computational studies of electrochemical interfaces based on density-functional theory (DFT) play an increasingly important role in present research on electrochemical processes for energy conversion and storage. The homogeneous background…
The dielectric response of nano-confined fluids is crucial across technologies and biological systems, yet its calculation and interpretation from molecular simulations are often muddled by unclear boundary conditions. We re-derive the…
The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations…
We consider the dynamics of particle systems where the particles are confined by impenetrable barriers to a bounded, possibly non-convex domain $\Omega$. When particles hit the boundary, we consider an instant change in velocity, which…
Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems…
In the present study, a discrete forcing Immersed Boundary Method (IBM) is proposed for the numerical simulation of high-speed flow problems including heat exchange. The flow field is governed by the compressible Navier-Stokes equations,…